[gmx-users] Questions regarding Polarization Energy Calculation
jesmin jahan
shraban03 at gmail.com
Fri Aug 17 17:14:32 CEST 2012
Hi Mark,
Thanks for your reply.
In the ffnonbonded.itp, I set all sigma and epsilon values to zero.
So, the the LJ energy is coming as zero. But the coulomb potential is
non zero. What should I do to make it zero?
Energies (kJ/mol)
GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic En.
-2.23121e+03 0.00000e+00 -3.47729e+04 -3.70041e+04 0.00000e+00
Total Energy Temperature Pressure (bar)
-3.70041e+04 0.00000e+00 0.00000e+00
One more point: I am not sure whether getting the 0 for an energy
does mean that it is not being calculated at all!
It seems, the energy value was calculated but the result was zero
because the sigma and epsilon were zero. In that case, the time
reported by the program will also include the time of the extra
calculation (unless the program is smart enough to know before hand
that the result is going to be zero and return from the top!). So,
while comparing with other molecular dynamic packages, its not fair to
report that time for gromacs which also includes non GB time (as that
can make Gromacs slower than others who do not include non GB-time).
Any suggestions about this? What is the fair approach for gromacs?
Thanks,
Jesmin
On Fri, Aug 17, 2012 at 12:00 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 17/08/2012 1:14 PM, jesmin jahan wrote:
>>
>> Hi Mark,
>>
>> According to your advice " remove the the bonded terms and zero the
>> VDW parameters",
>> I removed everything under [ bond] , [angles], [pairs] and [ dihedrals
>> ],
>
>
> This only removes the "bonded" terms (in the sense of those atoms that
> interact because of the presence of bonds). The VDW parameters for
> non-bonded interactions are in ffnonbonded.itp for your force field. You
> should probably follow the advice here
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Modifying_a_force_field
> to get a local copy you can change conveniently.
>
>
>> and run the simulation mdrun rerun.
>>
>> I got output something like the following:
>>
>>
>> Energies (kJ/mol)
>> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic
>> En.
>> -2.23121e+03 7.54287e+07 -3.47729e+04 7.53917e+07
>> 0.00000e+00
>> Total Energy Temperature Pressure (bar)
>> 7.53917e+07 0.00000e+00 0.00000e+00
>>
>> where the previous output was something like this:
>>
>> Energies (kJ/mol)
>> Bond Angle Proper Dih. Improper Dih.GB
>> Polarization
>> 2.12480e+03 4.80088e+02 1.06648e+03 9.04861e+01
>> -2.23122e+03
>> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>> Potential
>> 7.05695e+02 5.47366e+03 -4.16856e+02 -8.74797e+03
>> -1.45483e+03
>> Kinetic En. Total Energy Temperature Pressure (bar)
>> 0.00000e+00 -1.45483e+03 0.00000e+00 0.00000e+00
>>
>>
>>
>> Energies (kJ/mol)
>> GB Polarization LJ (SR) Coulomb (SR) Potential Kinetic
>> En.
>> -2.23121e+03 4.17621e+13 -3.47729e+04 4.17621e+13
>> 0.00000e+00
>> Total Energy Temperature Pressure (bar)
>> 4.17621e+13 0.00000e+00 0.00000e+00
>>
>>
>> So, you can see, although it has managed to remove some extra terms,
>> the LJ and Columb potential are still there. I searched for VWD
>> parameters. Although I saw various options for VWD, its not clear
>> from the options, how to turn it off. Could you kindly tell me more
>> clearly about it?
>>
>>
>> I was also looking into the forcefield.itp file. I set the gen-pairs
>> to no , fudgeLJ 1 and fudgeQQ to 1 which were yes, .5 and .83
>> respectively originally.
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> 1 2 no 1 1
>>
>> Please let me know how to get rid of calculation of other energies
>> (LJ, Culumb and Total Potential) and how to set the parameters for
>> this properly.
>
>
> You can't get rid of the total. It's the total. You're trying to keep the
> (GB) Coulomb.
>
> Mark
>
>
>>
>> Thanks for your help.
>>
>> Sincerely,
>> Jesmin
>> On Thu, Aug 16, 2012 at 3:27 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>> wrote:
>>>
>>> On 16/08/2012 5:08 PM, jesmin jahan wrote:
>>>>
>>>> Hi Mark,
>>>>
>>>> Thanks for your reply.
>>>> If I open the .tpr file using notepad, it seems to be a binary file.
>>>> Then, how to remove the the bonded terms and zero the VDW parameters?
>>>
>>>
>>> In the .top file from which you made the .tpr. (And contributing .itp
>>> files)
>>> Parts of chapter 5 may help with this process.
>>>
>>> Mark
>>>
>>>
>>>> I really need to compare how fast different well known package can
>>>> compute GB-polarization energy and how good the energy values are?
>>>> That's why time is an important factor me my experiments and I really
>>>> want to measure the time for GB energy in isolation !
>>>>
>>>> Thanks,
>>>> Jesmin
>>>>>
>>>>> On Thu, Aug 16, 2012 at 2:44 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>>>>> wrote:
>>>>>>
>>>>>> On 16/08/2012 4:26 PM, jesmin jahan wrote:
>>>>>>>
>>>>>>> Hi Mark,
>>>>>>>
>>>>>>> Thanks for your previous reply.
>>>>>>> I tried to run single point energy simulation with some proteins.
>>>>>>> I got .log files with content like this:
>>>>>>>
>>>>>>> Energies (kJ/mol)
>>>>>>> Bond Angle Proper Dih. Improper Dih.GB
>>>>>>> Polarization
>>>>>>> 1.54109e+04 3.84351e+03 8.47152e+03 3.58425e+02
>>>>>>> -1.69666e+04
>>>>>>> LJ-14 Coulomb-14 LJ (SR) Coulomb (SR)
>>>>>>> Potential
>>>>>>> 4.29664e+03 3.63997e+04 2.22900e+05 -5.18818e+04
>>>>>>> 2.22832e+05
>>>>>>> Kinetic En. Total Energy Temperature Pressure (bar)
>>>>>>> 1.08443e+09 1.08465e+09 2.73602e+07 0.00000e+00
>>>>>>> .......
>>>>>>>
>>>>>>> Computing: M-Number M-Flops %
>>>>>>> Flops
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>> Generalized Born Coulomb 0.005711 0.274
>>>>>>> 0.2
>>>>>>> GB Coulomb + LJ 0.416308 25.395
>>>>>>> 18.5
>>>>>>> Outer nonbonded loop 0.016367 0.164
>>>>>>> 0.1
>>>>>>> 1,4 nonbonded interactions 0.008410 0.757
>>>>>>> 0.6
>>>>>>> Born radii (HCT/OBC) 0.439486 80.426
>>>>>>> 58.5
>>>>>>> Born force chain rule 0.439486 6.592
>>>>>>> 4.8
>>>>>>> NS-Pairs 0.943653 19.817
>>>>>>> 14.4
>>>>>>> Reset In Box 0.003179 0.010
>>>>>>> 0.0
>>>>>>> CG-CoM 0.006358 0.019
>>>>>>> 0.0
>>>>>>> Bonds 0.003219 0.190
>>>>>>> 0.1
>>>>>>> Angles 0.005838 0.981
>>>>>>> 0.7
>>>>>>> Propers 0.011273 2.582
>>>>>>> 1.9
>>>>>>> Virial 0.003899 0.070
>>>>>>> 0.1
>>>>>>> Stop-CM 0.003179 0.032
>>>>>>> 0.0
>>>>>>> Calc-Ekin 0.006358 0.172
>>>>>>> 0.1
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>> Total 137.479
>>>>>>> 100.0
>>>>>>>
>>>>>>>
>>>>>>> -----------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>>>>>>>
>>>>>>> av. #atoms communicated per step for force: 2 x 6859.0
>>>>>>>
>>>>>>>
>>>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>>>>>
>>>>>>> Computing: Nodes Number G-Cycles Seconds %
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>> Domain decomp. 16 1 0.043 0.0
>>>>>>> 1.4
>>>>>>> Comm. coord. 16 1 0.003 0.0
>>>>>>> 0.1
>>>>>>> Neighbor search 16 1 0.103 0.0
>>>>>>> 3.5
>>>>>>> Force 16 1 1.530 0.5
>>>>>>> 51.5
>>>>>>> Wait + Comm. F 16 1 0.264 0.1
>>>>>>> 8.9
>>>>>>> Write traj. 16 1 0.062 0.0
>>>>>>> 2.1
>>>>>>> Update 16 1 0.001 0.0
>>>>>>> 0.0
>>>>>>> Comm. energies 16 2 0.933 0.3
>>>>>>> 31.4
>>>>>>> Rest 16 0.031 0.0
>>>>>>> 1.1
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>> Total 16 2.970 0.9
>>>>>>> 100.0
>>>>>>>
>>>>>>> -----------------------------------------------------------------------
>>>>>>>
>>>>>>> NOTE: 31 % of the run time was spent communicating energies,
>>>>>>> you might want to use the -gcom option of mdrun
>>>>>>>
>>>>>>>
>>>>>>> Parallel run - timing based on wallclock.
>>>>>>>
>>>>>>> NODE (s) Real (s) (%)
>>>>>>> Time: 0.056 0.056 100.0
>>>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>>>>>> Performance: 7.497 2.442 1.535 15.637
>>>>>>>
>>>>>>>
>>>>>>> >From the log file, it seems, the time includes the time for LJ and
>>>>>>> Columb Potential Energy. But as I said before, I am only interested
>>>>>>> to
>>>>>>> GB-energy times. I am doing a comparative study of GB-energy
>>>>>>> performance (values vs time) for different molecular dynamic
>>>>>>> packages.
>>>>>>
>>>>>>
>>>>>> Since the LJ calculation also needs the distances, GROMACS does them
>>>>>> in
>>>>>> the same loops and makes no apology for being efficient. :-) If you're
>>>>>> really trying to measure the time for the GB energy in isolation, then
>>>>>> you
>>>>>> will need to construct a different model physics that lacks LJ
>>>>>> interactions.
>>>>>> Or perhaps you don't really want to measure the time for GB energy in
>>>>>> isolation. Depends what you're planning on using the information for,
>>>>>> but
>>>>>> usually measuring a time representative of the calculation you plan to
>>>>>> run
>>>>>> later is a good way to avoid having to account for lots of subtleties
>>>>>> of
>>>>>> different packages.
>>>>>>
>>>>>>
>>>>>>> That's why I was trying to deduct the time for any other extra energy
>>>>>>> computation time from it.
>>>>>>>
>>>>>>> Can anyone tell me how to get the exact time of GB-polarization
>>>>>>> energy
>>>>>>> (including Born radii) and excluding the times for any other
>>>>>>> additional energy (like LJ and Columb etc) from gromacs simutation?
>>>>>>
>>>>>>
>>>>>> The .tpr you use for the rerun doesn't have to be one that will
>>>>>> produce
>>>>>> a sensible model physics. If you remove the bonded terms and zero the
>>>>>> VDW
>>>>>> parameters then the only thing left to compute is the electrostatics,
>>>>>> which
>>>>>> will give you the time you seek. You'll still potentially have time
>>>>>> spent
>>>>>> doing neighbour searching, and that is something you need to consider
>>>>>> for
>>>>>> gauging relative performance of different packages. Again, the times
>>>>>> you
>>>>>> measure will not be significant unless you run for at least several
>>>>>> minutes.
>>>>>>
>>>>>> Mark
>>>>>>
>>>>>>
>>>>>>> Thanks,
>>>>>>> Jesmin
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> On Tue, Aug 14, 2012 at 10:16 AM, jesmin jahan <shraban03 at gmail.com>
>>>>>>> wrote:
>>>>>>>>
>>>>>>>> Thanks Mark for your reply. I was trying to use Single-Point Energy
>>>>>>>> Calculation as you advised in your first reply but for most of the
>>>>>>>> files the simulation failed because I was using the original .pdb
>>>>>>>> files in the mdrun command.
>>>>>>>>
>>>>>>>> Anyways. I really appreciate your help.
>>>>>>>> Thanks again,
>>>>>>>> Jesmin
>>>>>>>>
>>>>>>>> On Tue, Aug 14, 2012 at 1:26 AM, Mark Abraham
>>>>>>>> <Mark.Abraham at anu.edu.au> wrote:
>>>>>>>>>
>>>>>>>>> On 14/08/2012 7:38 AM, jesmin jahan wrote:
>>>>>>>>>>
>>>>>>>>>> Dear Gromacs Users,
>>>>>>>>>>
>>>>>>>>>> I have some questions regarding GB-Polarization Energy Calculation
>>>>>>>>>> with Gromacs. I will be grateful if someone can help me with the
>>>>>>>>>> answers.
>>>>>>>>>>
>>>>>>>>>> I am trying to calculate GB-Polarization energy for different
>>>>>>>>>> Protein
>>>>>>>>>> molecules. I am interested both in energy values with the time
>>>>>>>>>> required to calculate the Born Radii and Polarization Energy.
>>>>>>>>>> I am not doing any energy minimization step as the files I am
>>>>>>>>>> using
>>>>>>>>>> as
>>>>>>>>>> input are already minimized.
>>>>>>>>>>
>>>>>>>>>> Here is the content of my mdrun.mdp file:
>>>>>>>>>>
>>>>>>>>>> constraints = none
>>>>>>>>>> integrator = md
>>>>>>>>>> pbc = no
>>>>>>>>>> dt = 0.001
>>>>>>>>>> nsteps = 0
>>>>>>>>>> implicit_solvent = GBSA
>>>>>>>>>> gb_algorithm = HCT
>>>>>>>>>> sa_algorithm = None
>>>>>>>>>>
>>>>>>>>>> And I am using following three steps for all the .pdb files I
>>>>>>>>>> have:
>>>>>>>>>>
>>>>>>>>>> let x is the name of the .pdb file.
>>>>>>>>>>
>>>>>>>>>> pdb2gmx -f x.pdb -ter -ignh -ff amber99sb -water none
>>>>>>>>>> grompp -f mdr.mdp -c conf.gro -p topol.top -o imd.tpr
>>>>>>>>>> mpirun -np 8 mdrun_mpi -deffnm imd -v -g x.log
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> So you're not using the advice I gave you about how to calculate
>>>>>>>>> single
>>>>>>>>> point energies. OK.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> 1 .Now the running time reported by a log file also includes other
>>>>>>>>>> times. Its also not clear to me whether the time includes the time
>>>>>>>>>> for
>>>>>>>>>> Born Radii calculations.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> The timing breakdown is printed at the end of the .log file. Likely
>>>>>>>>> your
>>>>>>>>> time is heavily dominated by the GB calculation and communication
>>>>>>>>> cost. Born
>>>>>>>>> radii calculation are part of the former, and not reported
>>>>>>>>> separately. You
>>>>>>>>> should not bother with timing measurements unless your run goes for
>>>>>>>>> at least
>>>>>>>>> several minutes, else your time will be dominated by I/O and setup
>>>>>>>>> costs.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> So, to get the GB-energy time I am doing the following: I am also
>>>>>>>>>> running a simulation with "implicit_solvent" set to "no" and I am
>>>>>>>>>> taking the difference of these two (with GB and Without GB). Is
>>>>>>>>>> that
>>>>>>>>>> a
>>>>>>>>>> right approach?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> No, that measures the weight difference between an apple and an
>>>>>>>>> orange, not
>>>>>>>>> whether the apple's seeds are heavy.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> I also want to be sure that it also includes Born-Radii
>>>>>>>>>> calculation
>>>>>>>>>> time.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> It's part of the GB calculation, so it's included in its timing.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Is there any other approach to do this?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> 2. I was trying to run the simulations on 192 cores (16 nodes each
>>>>>>>>>> with 12 codes). But I got "There is no domain decomposition for 12
>>>>>>>>>> nodes that is compatible with the given box and a minimum cell
>>>>>>>>>> size
>>>>>>>>>> of
>>>>>>>>>> 2.90226 nm" error for some pdb files. Can anyone explain what is
>>>>>>>>>> happening. Is there any restriction on number of nodes can be
>>>>>>>>>> used?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Yes. See discussion linked from
>>>>>>>>> http://www.gromacs.org/Documentation/Errors
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> 3. I run the simulations with 1 way 96 (8 nodes each with 12
>>>>>>>>>> cores).
>>>>>>>>>> Its not clear to me from the log file whether Gromacs is able to
>>>>>>>>>> utilize all the 92 cores. It seems, it is using only 8 nodes.
>>>>>>>>>> Does Gromacs use both shared and distributed memory parallelism?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Not at the moment. Look at the top of your .log file for clues
>>>>>>>>> about
>>>>>>>>> what
>>>>>>>>> your configuration is making available to GROMACS. It is likely
>>>>>>>>> that
>>>>>>>>> mpirun
>>>>>>>>> -np 8 makes only 8 MPI processes available to GROMACS. Using more
>>>>>>>>> will
>>>>>>>>> require you to use your MPI installation correctly (and we can't
>>>>>>>>> help
>>>>>>>>> with
>>>>>>>>> that).
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> 4. In the single-point energy calculation "mdrun -s input.tpr
>>>>>>>>>> -rerun configuration.pdb", is the configuration.pdb mentioned is
>>>>>>>>>> the
>>>>>>>>>> original pdb file used on pdb2gmx with -f option? Or its a
>>>>>>>>>> modified
>>>>>>>>>> pdb file? I am asking because if I use the original file that does
>>>>>>>>>> not
>>>>>>>>>> work always :-(
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> It can be any configuration that matches the .top file you gave to
>>>>>>>>> grompp.
>>>>>>>>> That's the point - you only need one run input file to compute the
>>>>>>>>> energy of
>>>>>>>>> any such configuration you later want. The configuration you gave
>>>>>>>>> to
>>>>>>>>> grompp
>>>>>>>>> (or any other tool) doesn't matter.
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> 5. Is there any known speedup factor of Gromacs on multicores?
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> That depends on your simulation system, hardware, network and
>>>>>>>>> algorithm.
>>>>>>>>> Don't bother with fewer than hundreds of atoms per core.
>>>>>>>>>
>>>>>>>>> Mark
>>>>>>>>> --
>>>>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>>>>> * Only plain text messages are allowed!
>>>>>>>>> * Please search the archive at
>>>>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>>>>>> * Please don't post (un)subscribe requests to the list. Use the www
>>>>>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>> Jesmin Jahan Tithi
>>>>>>>> PhD Student, CS
>>>>>>>> Stony Brook University, NY-11790.
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>> --
>>>>>> gmx-users mailing list gmx-users at gromacs.org
>>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>>> * Only plain text messages are allowed!
>>>>>> * Please search the archive at
>>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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>>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Jesmin Jahan Tithi
>>>>> PhD Student, CS
>>>>> Stony Brook University, NY-11790.
>>>>>
>>>>
>>>> --
>>>> Jesmin Jahan Tithi
>>>> PhD Student, CS
>>>> Stony Brook University, NY-11790.
>>>
>>>
>>> --
>>> gmx-users mailing list gmx-users at gromacs.org
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>>
>>
>>
>
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--
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.
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